bacgroundCorrect {blima} | R Documentation |
Background correction procedure selecting beads with background Intensity I_b |mean - I_b | > k*SD(I_bs) for exclusion.
bacgroundCorrect(b, normalizationMod = NULL, channelBackground = "GrnB", k = 3, channelBackgroundFilter = "bgf", channelAndVector = NULL)
b |
List of beadLevelData objects (or single object). |
normalizationMod |
NULL for normalization of all input b. Otherwise specifies logical vector of the length equals to the number of arrays in b or list of such vectors if b is a list of beadLevelData classes. |
channelBackground |
Name of channel to normalize. |
k |
Parameter of method stringency (default is 3). |
channelBackgroundFilter |
Filtered beads will have weight 0 and non filtered weight 1. |
channelAndVector |
Represents vector to bitvise multiple to the channelBackgroundFilter vector. |
Vojtěch Kulvait
if(require("blimaTestingData") && interactive()) { #To perform background correction on blimatesting object for two groups. Background correction is followed by correction for non positive data. Array spots out of selected groups will not be processed. data(blimatesting) #Prepare logical vectors corresponding to conditions A and E. groups1 = "A"; groups2 = "E"; sampleNames = list() c = list() for(i in 1:length(blimatesting)) { p = pData(blimatesting[[i]]@experimentData$phenoData) c[[i]] = p$Group %in% c(groups1, groups2); sampleNames[[i]] = p$Name } #Background correction and quantile normalization followed by testing including log2TransformPositive transformation. blimatesting = bacgroundCorrect(blimatesting, normalizationMod=c, channelBackgroundFilter="bgf") blimatesting = nonPositiveCorrect(blimatesting, normalizationMod=c, channelCorrect="GrnF", channelBackgroundFilter="bgf", channelAndVector="bgf") }else { print("To run this example, please install blimaTestingData package from bioconductor by running BiocManager::install('blimaTestingData')."); }